2008 Engineering review at Utah:Summary

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Home < 2008 Engineering review at Utah:Summary
  • Monday 24
  • Kick-off presentations and definition of open issues to be discussed. Main theme: a) Putting modules into workflow pipelines, running such pipelines on a large number of datasets using a batch processing and eventually grid capabilities. b) New methods from the Utah groups to be integrated into Slicer-3. Presentations by different groups on:
    • Slicer-3 architecture
    • Segmentation
    • DTI analysis
    • Shape analysis
  • Tuesday 25: Topics discussed in details:
    • Dicom to nrrd conversion, in particular with DWI data with different coordinate systems, gradient direction schemes, variable b-values and more. Agreed to run a "hard test" by taking new Siemens mosaic-format, multiple b-value DICOM data (Core-3 UNC autism project) and testing the existing conversion tool.
    • Quality control / Validation: Discussion of need to QC the nrrd DTI data (conversion correct?, tensors in correct orientation?, outlier detection?, artifact detection?). Group defined a need to work on QC methodology for data quality checking, to be run within Slicer-3 but maybe also as a stand-alone command-line as part of the data conversion and correction pipelines.
    • Workflow: Concepts of a workflow environment was discussed, using the example of DTI preprocessing and population-based analysis of DTI data. Need for two concepts, one for chaining of NAMIC modules, and one for running such chains/pipelines in a batch mode. Discussion of Batchmake versus capabilities of Grid computing.
    • Workflow in DWI preprocessing: DICOM to nrrd conversion, motion correction, Eddy current correction, linear registration to anatomical MRI or atlas space, robust calculation of tensor etc.: Would be unique NAMIC contribution to help all researchers. All pieces exist (nrrd Core-2, linear registration with scalar images by Jim Miller and itk modules, trnasformation of DWI and tensor fields via Francois and Casey, concatenation of transformations as planned (see Summary).
    • Workflow in DWI preprocessing: Discussion of population-based DWI analysis of white matter fiber bundles. Casey Goodlett has all modules in cvs repository, ready to be delivered as NAMIC modules, ready to be used in a NAMIC chaining architecture. Group registration of large set of images is using the MIT atlas-building code (Polina Golland, Sardar), preliminary tests are successful. The prototype of a fully automatic workflow for processing of DWI study is planned for the summer programming week end of June 2008 (see summary). Statistics is so far done with Matlab. Discussion on using "R" as statistics modules in Slicer-3.



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